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In virtual box 3.0.2 is there any performance difference between the native VDI format and VMDK?

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I don't think so - for example, this blog post claims the following:

Both formats are wrappers around a raw disk image so raw performance isn’t really at issue.

However, it also says the following:

VirtualBox has to mount a vmdk image as a writethrough disk, which means it loses things like snapshots and possibly driver performance.

I don't know if this applies to the newest version, but it sounds like you should go with VDI.

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VirtualBox 4 will take snapshots with a VMDK (I just tested it with 4.0.8) and it sounds like the feature has been in there since version 3. However, as it's not the native format for VirtualBox the implementation of some things will probably always lag. (For instance, even in 4.0.8 using VBoxManage modifyhd foo.vmdk --compact won't work, it's just for VDI.) So it is indeed probably best to use VDI. – Hostile Fork Jun 17 '11 at 3:17
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This isn't a performance related item, but VMDK is the native disk image format for VMWare. If you ever plan on using VMWare in the future, this is the disk format you will want to use.

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